Contacts of the helix formed by residues 280 - 301 (chain D) in PDB entry 5TT2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 280 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C THR* 5.7 6.0 - - - +
284C ARG* 4.6 12.1 - - + -
363C PHE* 3.5 36.8 - - + -
399C LEU* 4.9 2.2 - - + -
234D ASN* 4.4 4.0 + - - -
276D ARG 4.8 1.7 + - - +
277D GLY* 3.2 9.7 + - - -
278D LEU 3.1 0.4 - - - -
279D LYS* 1.3 81.0 - - + +
281D LEU* 1.3 64.4 + - - +
282D HIS* 3.3 5.2 - - - -
283D VAL* 3.3 14.0 - - + +
284D ARG* 3.1 43.5 + - - +
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Residues in contact with LEU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.3 23.8 - - + -
97D LEU* 5.3 2.5 - - + -
211D SER* 4.3 17.9 - - - -
212D PRO* 4.5 10.1 - - + -
213D TYR* 4.5 2.9 - - + -
227D TYR* 5.1 10.5 - - + +
277D GLY 3.6 2.4 + - - -
278D LEU* 3.1 33.6 + - + +
279D LYS 3.6 0.2 - - - -
280D THR* 1.3 78.0 - - - +
282D HIS* 1.3 58.2 + - - +
284D ARG* 3.6 21.9 - - - +
285D MET* 2.8 68.6 + - + +
501D SO4 5.2 0.7 - - - +
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Residues in contact with HIS 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LYS* 3.7 13.4 + - - -
399C LEU* 3.0 29.7 + - + +
37D PHE* 4.5 9.2 - - + -
38D ALA* 3.6 27.8 - - + +
41D ALA* 5.5 1.0 - - - +
42D ILE* 4.6 2.2 - - + -
213D TYR* 3.4 38.3 - - + +
278D LEU 4.7 2.0 + - - -
279D LYS 3.1 28.9 + - - -
280D THR* 4.3 2.0 - - - -
281D LEU* 1.3 80.8 + - - +
283D VAL* 1.3 84.9 + - + +
286D GLU* 3.0 36.0 + - - +
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Residues in contact with VAL 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C VAL* 3.8 41.9 - - + +
284C ARG* 4.7 8.5 - - + -
287C LYS* 3.7 31.9 - - + -
399C LEU* 4.8 5.4 - - + -
280D THR* 3.3 25.8 - - + +
282D HIS* 1.3 102.4 - - + +
284D ARG* 1.3 65.9 + - + +
286D GLU* 3.9 7.2 - - - +
287D LYS* 3.5 13.0 + - - +
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Residues in contact with ARG 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C THR* 4.6 8.7 - - + -
283C VAL* 4.9 3.1 - - + -
234D ASN* 3.6 20.5 + - - +
277D GLY 2.8 30.5 + - - -
278D LEU* 4.9 0.4 - - - +
280D THR* 3.1 31.4 + - - +
281D LEU* 3.6 31.2 - - - +
283D VAL* 1.3 78.6 - - + +
285D MET* 1.3 66.0 + - + +
287D LYS* 3.2 6.3 + - - +
288D HIS* 3.0 26.5 + - - -
363D PHE* 3.4 30.3 - - - -
399D LEU* 3.6 18.2 - - + +
501D SO4 2.7 47.8 + - - +
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Residues in contact with MET 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D SER* 3.7 25.1 - - - +
213D TYR* 3.7 12.1 - - + -
214D PHE* 3.5 25.3 - - + -
227D TYR* 5.7 2.9 - - - +
281D LEU* 2.8 49.6 + - + +
284D ARG* 1.3 71.7 - - - +
286D GLU* 1.3 60.2 + - - +
288D HIS* 3.2 32.6 + - + +
289D PHE* 2.8 29.8 + - - +
330D THR* 4.6 13.5 - - - -
501D SO4 3.9 21.5 - - - +
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D HIS* 3.1 25.6 + - - -
213D TYR* 2.6 32.5 + - - +
214D PHE* 4.3 3.7 - - - -
282D HIS 3.0 17.5 + - - +
283D VAL* 3.9 8.1 - - - +
285D MET* 1.3 77.3 - - - +
287D LYS* 1.3 51.5 + - - +
289D PHE* 3.2 15.3 + - - +
290D LYS* 2.7 36.2 + - - +
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Residues in contact with LYS 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ALA* 4.6 2.6 - - - +
282C HIS* 3.7 15.2 - - - -
283C VAL* 3.7 25.8 - - + -
283D VAL 3.5 3.6 + - - +
284D ARG 3.2 8.8 + - - +
286D GLU* 1.3 75.6 - - - +
288D HIS* 1.3 61.2 + - - +
290D LYS* 4.1 19.1 - - + +
291D ASN* 2.8 61.5 + - - +
399D LEU* 3.7 28.0 + - + -
400D GLU 3.5 16.1 + - - -
401D ASP* 4.8 4.0 + - - +
402D GLU* 5.2 1.8 - - - +
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Residues in contact with HIS 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D ARG 3.0 22.2 + - - -
285D MET* 3.3 30.1 - - + +
287D LYS* 1.3 77.0 - - - +
289D PHE* 1.3 55.3 + - - +
291D ASN* 4.2 0.5 - - - +
292D GLY* 2.9 27.7 + - - -
330D THR* 4.6 2.9 - - - -
331D GLY* 3.5 24.5 - - - +
361D GLY* 5.6 1.8 - - - -
362D GLY 3.3 23.6 - - - -
396D SER* 6.1 0.4 - - - -
397D VAL 2.9 25.0 + - - +
398D GLY* 3.8 5.8 + - - -
399D LEU* 3.5 21.2 - - + +
501D SO4 2.9 32.7 + - - -
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D PHE* 4.2 22.0 - + - -
33D HIS* 5.9 1.3 - + - -
214D PHE* 3.8 9.2 - + + -
285D MET 2.8 11.9 + - - +
286D GLU* 3.3 18.8 - - - +
288D HIS* 1.3 75.3 - - - +
290D LYS* 1.3 60.2 + - - +
292D GLY* 3.7 0.2 - - - -
293D MET* 2.8 50.6 + - + +
310D TYR* 3.4 11.2 - + - -
312D GLY* 4.8 0.4 - - - -
327D THR 4.6 3.4 - - - -
328D GLY* 3.6 19.1 - - - -
329D CYS* 3.1 50.4 + - + +
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Residues in contact with LYS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D GLU* 2.7 20.2 + - - +
287D LYS* 3.3 24.1 + - + +
289D PHE* 1.3 74.5 - - - +
291D ASN* 1.3 62.1 + - - +
293D MET* 3.6 5.6 + - - +
294D ALA* 3.2 21.3 + - - +
402D GLU* 4.7 16.0 + - - +
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Residues in contact with ASN 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D LYS* 2.8 42.1 + - - +
288D HIS 4.2 0.4 - - - +
290D LYS* 1.3 72.2 - - - +
292D GLY* 1.3 59.9 + - - +
294D ALA* 3.2 7.2 + - - +
295D VAL* 2.8 33.4 + - - +
397D VAL* 3.6 18.6 - - + -
398D GLY 3.1 19.6 + - - +
399D LEU* 3.8 2.6 - - - +
400D GLU 2.8 25.7 + - - +
402D GLU* 3.5 23.7 - - - +
405D LEU* 4.0 10.4 - - + +
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Residues in contact with GLY 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D HIS 2.9 19.7 + - - -
289D PHE 3.7 0.4 - - - -
291D ASN* 1.3 75.0 - - - +
293D MET* 1.3 57.5 + - - +
295D VAL* 3.3 1.9 + - - +
296D ALA* 2.8 32.6 + - - +
310D TYR* 4.0 13.2 - - - -
331D GLY* 4.4 2.2 - - - -
333D VAL* 3.7 15.4 - - - +
397D VAL* 4.0 12.1 - - - +
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Residues in contact with MET 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D PHE* 2.8 35.8 + - + +
290D LYS* 3.6 6.5 - - - +
292D GLY* 1.3 72.6 - - - +
294D ALA* 1.3 57.6 + - - +
296D ALA* 3.6 1.9 - - - +
297D GLN* 2.9 64.2 + - - +
310D TYR* 3.8 21.9 + - + -
312D GLY* 3.2 31.0 - - - +
313D LEU* 3.6 11.0 - - + -
314D PRO* 5.2 2.9 - - + -
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Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D LYS 3.2 8.3 + - - +
291D ASN* 3.2 9.7 + - - +
293D MET* 1.3 79.0 - - - +
295D VAL* 1.3 56.8 + - - +
297D GLN* 3.7 8.5 - - - +
298D PHE* 2.9 31.4 + - - +
402D GLU* 3.4 43.5 - - + +
406D LEU* 4.2 7.0 - - + +
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Residues in contact with VAL 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D ASN 2.8 22.2 + - - +
292D GLY 3.6 3.8 - - - +
294D ALA* 1.3 72.0 - - - +
296D ALA* 1.3 57.4 + - - +
298D PHE* 3.4 2.1 + - - +
299D LEU* 3.0 42.2 + - + +
333D VAL* 4.6 4.0 - - + -
354D PHE* 5.0 1.1 - - + -
395D LEU* 4.1 11.0 - - + -
397D VAL* 3.9 31.0 - - + -
405D LEU* 4.5 12.1 - - + -
406D LEU* 4.1 20.2 - - + -
409D LEU* 3.6 26.9 - - + -
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Residues in contact with ALA 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D GLY 2.8 20.6 + - - +
293D MET 3.6 3.4 - - - +
295D VAL* 1.3 73.3 - - - +
297D GLN* 1.3 62.4 - - - +
299D LEU* 3.3 3.4 + - - +
300D GLU* 3.0 25.5 + - - +
308D VAL* 4.1 4.3 - - + +
310D TYR* 3.5 33.0 - - + -
313D LEU* 3.7 17.8 - - + +
333D VAL* 4.1 13.9 - - + +
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Residues in contact with GLN 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D MET* 2.9 53.1 + - - +
294D ALA* 3.7 7.0 + - - +
296D ALA* 1.3 76.9 - - - +
298D PHE* 1.3 62.6 + - - +
300D GLU* 3.5 5.1 + - - +
301D SER* 3.2 23.6 + - - -
313D LEU* 4.1 14.1 - - + +
314D PRO* 5.9 1.0 - - - +
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Residues in contact with PHE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D ALA 2.9 17.9 + - - +
295D VAL 3.7 5.2 - - - +
297D GLN* 1.3 77.2 - - - +
299D LEU* 1.3 71.9 + - + +
301D SER* 3.1 19.3 + - - -
302D ASN* 3.1 36.5 + - - +
406D LEU* 3.8 42.4 - - + -
409D LEU* 4.1 12.8 - - + -
410D ASP* 3.5 39.5 - - + -
413D LEU* 4.5 5.4 - - + -
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Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D VAL* 3.0 39.0 + - + +
296D ALA 3.7 3.6 - - - +
298D PHE* 1.3 83.0 - - + +
300D GLU* 1.3 62.3 + - - +
302D ASN* 3.0 12.5 + - - +
305D VAL* 3.2 40.9 - - + +
308D VAL* 3.7 12.1 - - + -
333D VAL* 4.2 11.7 - - + -
335D PHE* 3.6 37.2 - - + -
395D LEU* 4.0 7.6 - - + -
409D LEU* 4.4 11.9 - - + -
413D LEU* 4.1 16.6 - - + -
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Residues in contact with GLU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ALA 3.0 16.8 + - - +
297D GLN* 3.9 6.1 - - - +
298D PHE 3.2 0.2 - - - -
299D LEU* 1.3 78.3 - - - +
301D SER* 1.3 57.7 + - - +
302D ASN 3.2 3.9 + - - +
305D VAL* 5.0 4.2 - - - +
307D LYS* 5.4 3.0 - - - +
308D VAL* 3.5 31.7 + - + +
313D LEU* 3.7 15.5 - - + +
314D PRO* 6.0 1.0 - - - +
315D SER* 3.0 37.5 + - - -
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Residues in contact with SER 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D GLN 3.2 11.8 + - - -
298D PHE* 3.1 14.5 + - - -
299D LEU 3.2 0.2 - - - -
300D GLU* 1.3 78.3 - - - +
302D ASN* 1.3 60.0 + - - +
303D PRO* 3.8 5.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il